Following the deaths, police imposed a curfew after thousands poured into the streets and torched a security vehicle and attacked a police station.
Renewed clashes erupted on Saturday when police fired teargas and used batons in an attempt to disperse demonstrators.
Mirwaiz Umar Farooq, a leading separatist figure and head of the region's main mosque, has demanded the resignation of the state's chief minister over the killings.
"All forces deployed in the state have to exercise utmost restraint while dealing with civilians"
Omar Abdullah, the chief minister in Kashmir
Omar Abdullah, the chief minister, "should resign because he has failed to protect the lives of Kashmiris", Farooq said.
"Abdullah's government is allowing India to oppress Kashmir," he said.
Friday's killings are the latest crisis to hit the government of Abdullah, who became chief minister of the volatile state 18 months ago.
Indian security forces have also been accused of killing three other civilians in the last two weeks.
In a statement released on Saturday, Abdullah said that "all forces deployed in the state have to exercise utmost restraint while dealing with civilians".
Farooq has called for the withdrawal of Indian army and paramilitary forces from civilian areas, arguing that "their presence fuels resentment".
India and Pakistan each rule a part of Kashmir but lay claim to the entire Himalayan territory.